Coding-Complete Genome Sequence of an African Swine Fever Virus Strain Liv13/33 Isolate from Experimental Transmission between Pigs and Ornithodoros moubata Ticks

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Coding-Complete Genome Sequence of an African Swine Fever Virus Strain Liv13/33 Isolate from Experimental

Transmission between Pigs and Ornithodoros moubata Ticks

Amélie Chastagner, Rémi Pereira de Oliveira, Evelyne Hutet, Mireille Le Dimna, Frédéric Paboeuf, Pierrick Lucas, Yannick Blanchard, Linda Dixon,

Laurence Vial, Marie-Frédérique Le Potier

To cite this version:

Amélie Chastagner, Rémi Pereira de Oliveira, Evelyne Hutet, Mireille Le Dimna, Frédéric Paboeuf, et al.. Coding-Complete Genome Sequence of an African Swine Fever Virus Strain Liv13/33 Isolate from Experimental Transmission between Pigs and Ornithodoros moubata Ticks. Microbiology Resource Announcements, American Society for Microbiology, 2020, 9 (17), �10.1128/MRA.00185-20�. �hal- 02618493�

Coding-Complete Genome Sequence of an African Swine Fever Virus Strain Liv13/33 Isolate from Experimental

Transmission between Pigs and Ornithodoros moubata Ticks

Amélie Chastagner,^aRémi Pereira de Oliveira,^a,b,cEvelyne Hutet,^aMireille Le Dimna,^aFrédéric Paboeuf,^dPierrick Lucas,^e Yannick Blanchard,^eLinda Dixon,^fLaurence Vial,^b,cMarie-Frédérique Le Potier^a

aSwine Virology and Immunology Unit, ANSES Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France

bUMR ASTRE, CIRAD, Montpellier, France

cUMR ASTRE, CIRAD, INRAE, University Montpellier, Montpellier, France

dSPF Pig Production and Experimentation Unit, ANSES Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France

eViral Genetic and Biosecurity Unit, ANSES Ploufragan-Plouzané-Niort Laboratory, Ploufragan, France

fOIE Reference Laboratory, The Pirbright Institute, Surrey, United Kingdom

ABSTRACT Here, we report the coding-complete genome sequence of African swine fever (ASF) virus strain Liv13/33, isolated from experimentally infected pigs andOrni- thodoros moubata ticks. The 11 sequences that we obtained harbored no notable differences to each other, and all of them were closely related to the genome se- quence of the Mkuzi 1979 strain of genotype I.

African swine fever is a contagious and highly lethal disease of pigs and wild suids caused by the African swine fever virus (ASFV) (Asfarviridae,Asfivirus) and may involve soft ticks of the Ornithodorosgenus as vectors and reservoirs of the virus (1).

The strain Liv13/33 was initially isolated in 1983 from a tick of the Ornithodoros moubata group in Livingstone (Zambia, Africa) (2, 3). This strain was previously se- quenced on two genes (B646L/P72 and E182L/P54) and identified as belonging to the genotype I (4, 5). The coding-complete genome sequence of Liv13/33 presented in this report was obtained from samples of a study that experimentally tested the vector competence ofO. moubata sensu strictoticks on pigs as previously described (6). Three 7-week-old specific-pathogen-free (SPF) Large White pigs were inoculated by the intramuscular route with a 10⁴ of the 50% hemadsorbing dose (HAD₅₀) of the ASFV Liv13/33 strain. Two hundred and sixty ASFV-free ticks were engorged on infected pigs on the first day of hyperthermia, when pig viremia ranged from 10^7.8to 10^8.1HAD₅₀/ml.

Five engorged ticks were frozen 3 months postinfection for sequencing analysis, and the others were fed on three new SPF pigs to assess their ability to transmit ASFV to naive pigs. These pigs displayed hyperthermia 2 days after being bitten by infected ticks.

Animal experiments performed at the air-filtered biosafety level 3 animal facilities at ANSES-Ploufragan were authorized by the French Ministry for Research (project no.

2017062615498464) and approved by the national ethics committee (authorization no.

11/07/17-3).

DNA was extracted using the High Pure PCR template preparation kit (Roche Life Science) from 400␮l of heparin blood samples collected from the six pigs during the viremia peak and from supernatants of crushed ticks prepared by filtration at 0.45␮m.

All samples were sequenced at the ANSES Institute (Ploufragan, France) with Proton Ion Torrent technology (Thermo Fisher Scientific, Frederick, MD). Individual libraries were created for each of the 6 pig samples and each of the 5 infected ticks for a total of 11

CitationChastagner A, Pereira de Oliveira R, Hutet E, Le Dimna M, Paboeuf F, Lucas P, Blanchard Y, Dixon L, Vial L, Le Potier M-F. 2020.

Coding-complete genome sequence of an African swine fever virus strain Liv13/33 isolate from experimental transmission between pigs andOrnithodoros moubataticks. Microbiol Resour Announc 9:e00185-20.https://doi.org/

10.1128/MRA.00185-20.

EditorSimon Roux, DOE Joint Genome Institute

Copyright© 2020 Chastagner et al. This is an open-access article distributed under the terms of theCreative Commons Attribution 4.0 International license.

Address correspondence to Marie-Frédérique Le Potier, [email protected].

Received5 March 2020 Accepted2 April 2020 Published23 April 2020

GENOME SEQUENCES

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libraries. The libraries for sequencing were prepared using the Ion Xpress plus fragment library kit and Ion Xpress barcode adapters 1-96 kit (Thermo Fisher Scientific). Magnetic beads from the Agencourt AMPure XP kit (Beckman Coulter, Villepinte, France) were used for DNA purification steps. The resulting reads were cleaned with Trimmomatic version 0.36 (options: ILLUMINACLIP: oligos.fasta: 2:30:5:1: true; LEADING: 3; TRAILING:

3; MAXINFO: 40:0.2; MINLEN: 36) and were firstde novoassembled using the SPAdes version 3.10.0 (option: – careful -t 12 -m 50) and MIRA version 4.0.2 (option:

IONTOR_SETTINGS -ASSEMBLY:mrpc⫽100) programs. In parallel, reads were mapped on three reference ASFV genomes of genotype I (BA71 [GenBank accession no. KP055815], Mkuzi 1979 [AY261362], and Benin97/1 [AM712239]) using Burrows- Wheeler Aligner software version 0.7.15-r1140 (option: mem -M). For each library, contigs produced by the different methods were scaffolded to generate a single consensus sequence validated by an additional BWA alignment.De novoassemblers and alignment software could not deal with inverted terminal repeats (ITRs) present in the ASFV genomes (7); the obtained sequence was thus probably shorter than that in reality. A comparison of the 11 genomes obtained showed fewer than 7 nucleotide differences that were mainly in ITRs and up to 34 gaps located in mononucleotide repeats A or T (Table 1). The coding-complete genome sequence of Liv13/33 with the best coverage (72.09⫻) was isolated from tick OmLF2 (Table 1).

This sequence of 188,277 bp (G⫹C content of 38.4%) harbored 228 open reading frames (ORFs) annotated with the help of Prokka (Galaxy version 1.13) based on the annotations of genomes available on the African Swine Fever Virus Database (http://asfvdb.popgenetics.net/), which proposed the most complete and homoge- neous revised annotation (8).

Data availability.The coding-complete genome sequence of isolate OmLF2 has been deposited in GenBank under the accession no.MN913970. Raw data from the 11 isolates for this project can be found in the GenBank SRA under accession no.

PRJNA587575.

ACKNOWLEDGMENTS

We are grateful to Vectopole Sud for funding the insectary whereO. moubatawas raised and to the Direction Générale de l’Alimentation for the financial support to CIRAD. We are thankful to CIRAD and ANSES for funding the Ph.D. grant of R. Pereira de Oliveira. We are also thankful to the NSF-NIH-EEID ASF project (grant no. 2019- 67015-28981) for their financial support to the publication of this research. This article is based upon work from COST Action ASF-STOP, supported by COST (European Cooperation in Science and Technology;www.cost.eu).

We thank the technical staff of CIRAD laboratory for raising the ASFV-free ticks as well as staff of the SPPAE Unit for animal care and sampling at ANSES-Ploufragan.

TABLE 1Description of Liv13/33 libraries generated in this study

Isolate Host

Total no. of produced reads

Total no. of mapped reads

Mean coverage^a on reference sequence OmLF2^b

No. of nucleotide differences/

gaps compared to reference sequence OmLF2^b

BioSample accession no.

SRA accession no.

6517IM SPF pig inoculated by the intramuscular route

7,629,638 26,960 18.70 2/17 SAMN13195023 SRS6053714

6524IM SPF pig inoculated by the intramuscular route

8,281,778 23,558 14.67 1/5 SAMN13195024 SRS6053715

6540IM SPF pig inoculated by the intramuscular route

11,118,211 47,712 32.69 0/6 SAMN13195025 SRS6053707

OmLF1 InfectedO. moubatatick 8,013,796 33,325 19.54 6/30 SAMN13191038 SRS6053706

OmLF2 InfectedO. moubatatick 13,675,689 129,761 72.16 Reference SAMN13191036 SRS6053705

OmLF3 InfectedO. moubatatick 5,526,024 27,692 16.83 7/34 SAMN13191040 SRS6053708

OmLM1 InfectedO. moubatatick 7,096,453 29,221 18.93 2/5 SAMN13191039 SRS6053709

OmLM2 InfectedO. moubatatick 3,742,020 33,372 21.39 0/8 SAMN13191042 SRS6053710

6573T SPF pig infected by ticks 12,708,781 26,414 17.14 1/10 SAMN13194022 SRS6053712

6594T SPF pig infected by ticks 7,616,042 25,491 17.81 0/10 SAMN13195022 SRS6053713

893T SPF pig infected by ticks 9,392,643 29,607 21.65 3/9 SAMN13191216 SRS6053711

aThe mean coverage corresponds to the mean number of reads mapped on the sequence of reference by position.

bGenBank accession no.MN913970.

Chastagner et al.

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